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tcR: an R package for T cell receptor repertoire advanced data analysis.
Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Lebedev YB, Mamedov IZ. Nazarov VI, et al. Among authors: chudakov dm. BMC Bioinformatics. 2015 May 28;16(1):175. doi: 10.1186/s12859-015-0613-1. BMC Bioinformatics. 2015. PMID: 26017500 Free PMC article.
Local fitness landscape of the green fluorescent protein.
Sarkisyan KS, Bolotin DA, Meer MV, Usmanova DR, Mishin AS, Sharonov GV, Ivankov DN, Bozhanova NG, Baranov MS, Soylemez O, Bogatyreva NS, Vlasov PK, Egorov ES, Logacheva MD, Kondrashov AS, Chudakov DM, Putintseva EV, Mamedov IZ, Tawfik DS, Lukyanov KA, Kondrashov FA. Sarkisyan KS, et al. Among authors: chudakov dm. Nature. 2016 May 19;533(7603):397-401. doi: 10.1038/nature17995. Epub 2016 May 11. Nature. 2016. PMID: 27193686 Free PMC article.
Exploring the pre-immune landscape of antigen-specific T cells.
Pogorelyy MV, Fedorova AD, McLaren JE, Ladell K, Bagaev DV, Eliseev AV, Mikelov AI, Koneva AE, Zvyagin IV, Price DA, Chudakov DM, Shugay M. Pogorelyy MV, et al. Among authors: chudakov dm. Genome Med. 2018 Aug 25;10(1):68. doi: 10.1186/s13073-018-0577-7. Genome Med. 2018. PMID: 30144804 Free PMC article.
HLA binding of self-peptides is biased towards proteins with specific molecular functions.
Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Scherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. Karnaukhov V, et al. Among authors: chudakov dm. bioRxiv [Preprint]. 2021 Feb 17:2021.02.16.431395. doi: 10.1101/2021.02.16.431395. bioRxiv. 2021. PMID: 33619495 Free PMC article. Preprint.
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2.
Goncharov M, Bagaev D, Shcherbinin D, Zvyagin I, Bolotin D, Thomas PG, Minervina AA, Pogorelyy MV, Ladell K, McLaren JE, Price DA, Nguyen THO, Rowntree LC, Clemens EB, Kedzierska K, Dolton G, Rius CR, Sewell A, Samir J, Luciani F, Zornikova KV, Khmelevskaya AA, Sheetikov SA, Efimov GA, Chudakov D, Shugay M. Goncharov M, et al. Nat Methods. 2022 Sep;19(9):1017-1019. doi: 10.1038/s41592-022-01578-0. Nat Methods. 2022. PMID: 35970936 No abstract available.
HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes.
Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Shcherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. Karnaukhov V, et al. Among authors: chudakov dm. Front Immunol. 2022 Dec 20;13:1067463. doi: 10.3389/fimmu.2022.1067463. eCollection 2022. Front Immunol. 2022. PMID: 36605212 Free PMC article.
Distinct organization of adaptive immunity in the long-lived rodent Spalax galili.
Izraelson M, Metsger M, Davydov AN, Shagina IA, Dronina MA, Obraztsova AS, Miskevich DA, Mamedov IZ, Volchkova LN, Nakonechnaya TO, Shugay M, Bolotin DA, Staroverov DB, Sharonov GV, Kondratyuk EY, Zagaynova EV, Lukyanov S, Shams I, Britanova OV, Chudakov DM. Izraelson M, et al. Among authors: chudakov dm. Nat Aging. 2021 Feb;1(2):179-189. doi: 10.1038/s43587-021-00029-3. Epub 2021 Feb 8. Nat Aging. 2021. PMID: 37118630
Targeted depletion of TRBV9+ T cells as immunotherapy in a patient with ankylosing spondylitis.
Britanova OV, Lupyr KR, Staroverov DB, Shagina IA, Aleksandrov AA, Ustyugov YY, Somov DV, Klimenko A, Shostak NA, Zvyagin IV, Stepanov AV, Merzlyak EM, Davydov AN, Izraelson M, Egorov ES, Bogdanova EA, Vladimirova AK, Iakovlev PA, Fedorenko DA, Ivanov RA, Skvortsova VI, Lukyanov S, Chudakov DM. Britanova OV, et al. Among authors: chudakov dm. Nat Med. 2023 Nov;29(11):2731-2736. doi: 10.1038/s41591-023-02613-z. Epub 2023 Oct 23. Nat Med. 2023. PMID: 37872223 Free PMC article.
172 results